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Certainly there is a lot of $2$-torsion. One easy way to construct such an example is to look at the embedding of the string link cobordism group on $n$ strands into the homology cobordism group of genus $n$. (Levine explains this embedding in his paper "Homology cylinders: an enlargment of the mapping class group." See Theorem 4 of that paper.) The string link group has lots of $2$-torsion. For example just tie an amphicheiral knot (which is not slice) into one of the strands. In fact the knot concordance group has infinitely many $\mathbb Z_2$ summands which inject into the homology cylinder group.

Thank you! You helps me a lot. Is there any other example, for surfaces with boundary ?
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hjjangMay 11 '12 at 14:16

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@HJ: this construction is for surfaces with one boundary component. I am sure there are other examples too. This paper arxiv.org/abs/0909.5580 shows there are infinitely many $\mathbb Z_2$ invariants, which should be realizable by actual homology cylinders, though I don't know off the top of my head.
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Jim ConantMay 11 '12 at 14:42

@Conant: Would there be more example for more boundary componant?
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hjjangMay 12 '12 at 7:18

@HJ: Sure. The map from string links to homology cobordisms extends to arbitrary numbers of components. Also, a string link is a homology cobordism of a planar surface so you get lots of direct examples that way.
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Jim ConantMay 12 '12 at 12:15